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Man Pages


Manual Reference Pages  -  BIO::TOOLS::RUN::EMBOSSAPPLICATION (3)

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NAME

Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications

CONTENTS

SYNOPSIS



  use Bio::Factory::EMBOSS;
  # get an EMBOSS application object from the EMBOSS factory
  $factory = Bio::Factory::EMBOSS->new();
  $application = $factory->program(embossversion);
  # run the application with an optional hash containing parameters
  $result = $application->run(); # returns a string or creates a file
  print $result . "\n";

  $water = $factory->program(water);

  # here is an example of running the application
  # water can compare 1 seq against 1->many sequences
  # in a database using Smith-Waterman
  my $seq_to_test;     # this would have a seq here
  my @seqs_to_check; # this would be a list of seqs to compare

  my $wateroutfile = out.water;
  $water->run({-sequencea => $seq_to_test,
               -seqall    => \@seqs_to_check,
               -gapopen   => 10.0,
               -gapextend => 0.5,
               -outfile   => $wateroutfile});
  # now you might want to get the alignment
  use Bio::AlignIO;
  my $alnin = Bio::AlignIO->new(-format => emboss,
                                              -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }



DESCRIPTION

The EMBOSSApplication class can represent EMBOSS any program. It is created by a Bio::Factory::EMBOSS object.

If you want to check command line options before sending them to the program set $prog->verbose to positive integer. The ADC description of the available command line options is then parsed in and compared to input.

See also Bio::Factory::EMBOSS and Bio::Tools::Run::EMBOSSacd.

FEEDBACK

    Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.



  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists



    Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

    Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:



  http://redmine.open-bio.org/projects/bioperl/



AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

    CONTRIBUTORS

Email: jason-AT-bioperl_DOT_org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

    run



 Title   : run
 Usage   : $embossapplication->run($attribute_hash)
 Function: Runs the EMBOSS program.
 Returns : string or creates files for now; will return objects!
 Args    : hash of input to the program



    acd



 Title   : acd
 Usage   : $embossprogram->acd
 Function: finds out all the possible qualifiers for this
           EMBOSS application. They can be used to debug the
           options given.
 Throws  :
 Returns : boolean
 Args    :



    name



 Title   : name
 Usage   : $embossprogram->name
 Function: sets/gets the name of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.
 Throws  :
 Returns : name string
 Args    : None



    descr



 Title   : descr
 Usage   : $embossprogram->descr
 Function: sets/gets the descr of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.
 Throws  :
 Returns : description string
 Args    : None



    group



 Title   : group
 Usage   : $embossprogram->group
 Function: sets/gets the group of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.

           If the application is assigned into a subgroup
           use l<subgroup> to get it.
 Throws  :
 Returns : string, group name
 Args    : group string



    subgroup



 Title   : subgroup
 Usage   : $embossprogram->subgroup
 Function: sets/gets the subgroup of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.
 Throws  :
 Returns : string, subgroup name; undef if not defined
 Args    : None



    program_dir



 Title   : program_dir
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Name of directory with EMBOSS programs
 Args    :



    program_path



 Title   : program_path
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Full path of program
 Args    :



    executable



 Title   : executable
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Name of program
 Args    :



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perl v5.20.3 BIO::TOOLS::RUN::EMBOSSAPPLICATION (3) 2016-04-05

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